Qualisys Holding Ab · OMXSTO:QSYS
Qualisys Holding Ab — Technical Presentation (February 2021)
18 slides from Qualisys Holding Ab's technical presentation, Feb 18, 2021
Slide 1: OpenSim and Qualisys
OpenSim and Qualisys Simplify your workflow with QTM and OpenSim Prepare data recorded with QTM for use in OpenSim Webinar 18th February 2021 Presented by
Slide 2: Presenters
Nils Betzler (PhD) Product Manager Life Sciences, Qualisys AB, Sweden Team Leader Application Solutions Ursula Trinler (PhD) Graduate Research Fellow, BG Klinik Ludwighafen, Germany Head of the movement science laboratory
Slide 3: Outline
Outline • Introduction to OpenSim - File formats and available tools - Example 1: Importing c3d files with OpenSim API and Matlab • Introduction to Qualisys Project Automation Framework (PAF) - Example 2: Importing c3d files with PAF, OpenSim API and Python • Summary
Slide 4: Introduction & Example 1
QUALISYS Introduction & Example 1
Slide 5: What is OpenSim?
What is OpenSim? Freely available, easy-to-use, extensible software for - developing models of musculoskeletal structures - creating dynamic simulation of movements - controlling and analyzing the neuromusculoskeletal system → Revealing muscle contributions to propulsion and support → How much muscl
Slide 6: OpenSim in more detail
OpenSim in more detail Input Simulation Output Experimental marker and force data (Qualisys) Trinler, 2019 Joint angles, Joint moments, Joint reaction forces, Muscle activations/forces…
Slide 7: File formats needed for OpenSim input
File formats needed for OpenSim input .trc for position of markers .mot files for markers and ground reaction force data
Slide 8: Available tools over the OpenSim community
Available tools over the OpenSim community MOtoNMS: Matlab Motion data elaboration Toolbox for NeuroMusculoSkeletal apps (https://simtk.org/projects/motonms)
Slide 9: Using OpenSim to process your c3d data (OpenSim API)
Using OpenSim to process your c3d data (OpenSim API) https://simtk.org/api_docs/opensim/api_docs/ C3D reading and conversion into OpenSim formats is available from OpenSim 4.0 →Uses Biomechanical Toolkit (BTK) (http://biomechanical-toolkit.github.io/) →Matlab or Python →Only supports reading Type-2
Slide 10: Example 1: Import C3D files with OpenSim 4.2 - MATLAB
EXAMPLE 1 Import C3D files with OpenSim 4.2 - MATLAB Export C3D file Import C3D file Import .trc and .mot (pre-filtering in QTM) Use OpenSim API Run simulation Export .trc and .mot
Slide 11: Matlab workflow
Matlab workflow Locate Matlab files in OpenSim folder (in Documents) Use c3dexport.m Review osimc3d.m for details Run in Matlab to generate .trc and .mot file
Slide 12: Project Automation Framework & Example 2
Project Automation Framework & Example 2
Slide 13: What is the Project Automation Framework (PAF)?
What is the Project Automation Framework (PAF)? • Set of tools to automate repetitive analysis steps • Part of Qualisys Track Manager (QTM) • Qualisys Analysis Modules1 are based on PAF: - Gait - Functional Assessment - Baseball - Golf - Cycling - Equine • Framework available to set up your own work
Slide 14: Example 2: Import C3D files with OpenSim 4.2 - Python
EXAMPLE 2 Import C3D files with OpenSim 4.2 - PYTHON Export C3D file Import .trc and .mot (pre-filtering in QTM) Run simulation Import C3D file Use OpenSim API Export .trc and .mot
Slide 15: Python workflow
Python workflow Download example from Github Install Python & OpenSim Link Python & OpenSim Open example project in QTM Use demo files or record your own Filter marker data in QTM (if desired) Generate .trc and .mot files Preview experimental data in OpenSim Scale model, run IK and Inverse Dynamics
Slide 16: Summary: Things to keep in mind
Summary Things to keep in mind →Is my experimental data clean? Do I need to use a filter? →Zero force plate before export from QTM (if possible) →Does the coordination system of my laboratory and OpenSim match each other? If not, adjust in the .m or .py file →Visualize the data in the OpenSim GUI: 1
Slide 17: Summary
Summary • Different options to prepare Qualisys data for OpenSim via OpenSim API - Matlab - Python (& PAF) • Starting point for your work in OpenSim • Let us know your feedback: - Github - support@qualisys.com - Personal (nils.Betzler@qualisys.com & Ursula.Trinler@bgu-ludwigshafen.de) Thank you for
Slide 18: References
References • Schellenberg F, Taylor WR, Trepczynski A, List R, Kutzner I, Schütz P, Duda GN, Lorenzetti S. Evaluation of the accuracy of musculoskeletal simulation during squats by means of instrumented knee prostheses. Med Eng Phys. 2018 Nov;61:95-99. doi: 10.1016/j.medengphy.2018.09.004. Epub 2018